Eggs-particularly egg yolks-are a rich source of bioactive nutrients and dietary compounds that influence metabolic health, lipid metabolism, immune function, and hematopoiesis. We investigated the effects of consuming an egg-free diet, three egg whites per day, and three whole eggs per day for 4 weeks on comprehensive clinical metabolic, immune, and hematologic profiles in young, healthy adults (18-35 y, BMI < 30 kg/m² or <30% body fat for men and <40% body fat for women, n = 26) in a 16-week randomized, crossover intervention trial. We observed that average daily macro- and micronutrient intake significantly differed across egg diet periods, including greater intake of choline during the whole egg diet period, which corresponded to increased serum choline and betaine without altering trimethylamine N-oxide. Egg white and whole egg intake increased serum isoleucine while whole egg intake reduced serum glycine-markers of increased and decreased risk of insulin resistance, respectively-without altering other markers of glucose sensitivity or inflammation. Whole egg intake increased a subset of large HDL particles (H6P, 10.8 nm) and decreased the total cholesterol:HDL-cholesterol ratio and % monocytes in female participants using combined oral contraceptive (COC) medication (n = 11) as compared to female non-users (n = 10). Whole egg intake further increased blood hematocrit whereas egg white and whole egg intake reduced blood platelet counts. Changes in clinical immune cell counts between egg white and whole egg diet periods were negatively correlated with several HDL parameters yet positively correlated with measures of triglyceride-rich lipoproteins and insulin sensitivity. Overall, the intake of whole eggs led to greater overall improvements in micronutrient diet quality, choline status, and HDL and hematologic profiles while minimally-yet potentially less adversely-affecting markers of insulin resistance as compared to egg whites.